java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, NamedSBase
, SBase
, UniqueNamedSBase
, UniqueSId
, IdManager
, TreeNodeWithChangeSupport
public class ModelDefinition extends Model
Model
s.
However, modelDefinitions are non-instantiated models
that can be called by submodels within the Model
class of an SBML document, or can be called externally
with references stored in ExternalModelDefinition
s.
JSBML_WRONG_SBO_TERM
Constructor | Description |
---|---|
ModelDefinition() |
Creates a new
ModelDefinition instance. |
ModelDefinition(int level,
int version) |
Creates a new
ModelDefinition instance. |
ModelDefinition(java.lang.String id) |
Creates a new
ModelDefinition instance. |
ModelDefinition(java.lang.String id,
int level,
int version) |
Creates a new
ModelDefinition instance. |
ModelDefinition(Model model) |
Creates a new
ModelDefinition instance cloned from the given core Model instance. |
Modifier and Type | Method | Description |
---|---|---|
ModelDefinition |
clone() |
Creates a deep copy of this object, i.e., a new
SBase with the same
properties
like this one. |
void |
init() |
isValidId
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm
addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet
accept, addCompartment, addCompartmentType, addConstraint, addEvent, addFunctionDefinition, addInitialAssignment, addParameter, addReaction, addRule, addSpecies, addSpeciesType, addUnitDefinition, addUnitDefinitionOrReturnIdenticalUnit, containsCompartment, containsFunctionDefinition, containsParameter, containsQuantity, containsReaction, containsSpecies, containsUniqueNamedSBase, containsUnitDefinition, createAlgebraicRule, createAssignmentRule, createCompartment, createCompartment, createCompartmentType, createCompartmentType, createConstraint, createDelay, createEvent, createEvent, createEventAssignment, createFunctionDefinition, createFunctionDefinition, createInitialAssignment, createKineticLaw, createKineticLawParameter, createKineticParameter, createModifier, createModifier, createParameter, createParameter, createProduct, createProduct, createRateRule, createReactant, createReactant, createReaction, createReaction, createSpecies, createSpecies, createSpecies, createSpecies, createSpeciesType, createSpeciesType, createTrigger, createUnit, createUnit, createUnitDefinition, createUnitDefinition, equals, findCallableSBase, findIdentical, findLocalParameters, findModifierSpeciesReference, findNamedSBase, findNamedSBaseWithDerivedUnit, findQuantity, findQuantityWithUnit, findReactionsForLocalParameter, findSimpleSpeciesReference, findSpeciesReference, findSymbol, findUniqueNamedSBase, findUniqueSBase, findUnitDefinition, findVariable, getAllowsChildren, getAreaUnits, getAreaUnitsInstance, getAssignmentRuleByVariable, getChildAt, getChildCount, getCompartment, getCompartment, getCompartmentCount, getCompartmentType, getCompartmentType, getCompartmentTypeCount, getConstraint, getConstraintCount, getConversionFactor, getConversionFactorInstance, getDelayCount, getElementBySId, getEvent, getEvent, getEventAssignmentCount, getEventCount, getExtentUnits, getExtentUnitsInstance, getFunctionDefinition, getFunctionDefinition, getFunctionDefinitionCount, getInitialAssignment, getInitialAssignment, getInitialAssignmentById, getInitialAssignmentBySymbol, getInitialAssignmentCount, getKineticLawCount, getLengthUnits, getLengthUnitsInstance, getListOfCompartments, getListOfCompartmentTypes, getListOfConstraints, getListOfCount, getListOfEvents, getListOfFunctionDefinitions, getListOfInitialAssignments, getListOfParameters, getListOfPredefinedUnitDefinitions, getListOfReactions, getListOfRules, getListOfSpecies, getListOfSpeciesTypes, getListOfUnitDefinitions, getLocalParameterCount, getMathContainerCount, getModelHistory, getModifierSpeciesReferenceCount, getModifierSpeciesReferences, getNamedSBaseCount, getNamedSBaseWithDerivedUnitCount, getNumCompartments, getNumCompartmentTypes, getNumConstraints, getNumDelays, getNumEventAssignments, getNumEvents, getNumFunctionDefinitions, getNumInitialAssignments, getNumKineticLaws, getNumListsOf, getNumLocalParameters, getNumMathContainers, getNumModifierSpeciesReferences, getNumNamedSBases, getNumNamedSBasesWithDerivedUnit, getNumParameters, getNumQuantities, getNumQuantitiesWithUnit, getNumReactions, getNumRules, getNumSBases, getNumSBasesWithDerivedUnit, getNumSpecies, getNumSpeciesReferences, getNumSpeciesTypes, getNumSpeciesWithBoundaryCondition, getNumStoichiometryMath, getNumSymbols, getNumTriggers, getNumUnitDefinitions, getNumUnits, getNumVariables, getParameter, getParameter, getParameterCount, getPredefinedUnitDefinition, getQuantityCount, getQuantityWithUnitCount, getRateRuleByVariable, getReaction, getReaction, getReactionCount, getRule, getRule, getRuleById, getRuleByVariable, getRuleCount, getSBaseById, getSBaseCount, getSBaseWithDerivedUnitCount, getSpecies, getSpecies, getSpeciesCount, getSpeciesReferenceCount, getSpeciesType, getSpeciesType, getSpeciesTypeCount, getSpeciesWithBoundaryConditionCount, getStoichiometryMathCount, getSubstanceUnits, getSubstanceUnitsInstance, getSymbolCount, getTimeUnits, getTimeUnitsInstance, getTriggerCount, getUnitCount, getUnitDefinition, getUnitDefinition, getUnitDefinitionById, getUnitDefinitionCount, getVariableCount, getVolumeUnits, getVolumeUnitsInstance, hashCode, hasUnit, initDefaults, initDefaults, isIdMandatory, isListOfCompartmentsEmpty, isListOfCompartmentTypesEmpty, isListOfConstraintsEmpty, isListOfEventsEmpty, isListOfFunctionDefinitionsEmpty, isListOfInitialAssignmentsEmpty, isListOfParametersEmpty, isListOfReactionsEmpty, isListOfRulesEmpty, isListOfSpeciesEmpty, isListOfSpeciesTypesEmpty, isListOfUnitDefinitionEmpty, isSetAreaUnits, isSetAreaUnitsInstance, isSetConversionFactor, isSetConversionFactorInstance, isSetExtentUnits, isSetExtentUnitsInstance, isSetLengthUnits, isSetLengthUnitsInstance, isSetListOfCompartments, isSetListOfCompartmentTypes, isSetListOfConstraints, isSetListOfEvents, isSetListOfFunctionDefinitions, isSetListOfInitialAssignments, isSetListOfParameters, isSetListOfReactions, isSetListOfRules, isSetListOfSpecies, isSetListOfSpeciesTypes, isSetListOfUnitDefinitions, isSetModelHistory, isSetSubstanceUnits, isSetSubstanceUnitsInstance, isSetTimeUnits, isSetTimeUnitsInstance, isSetVolumeUnits, isSetVolumeUnitsInstance, readAttribute, register, remove, removeCompartment, removeCompartment, removeCompartmentType, removeCompartmentType, removeConstraint, removeEvent, removeEvent, removeFunctionDefinition, removeFunctionDefinition, removeInitialAssignment, removeParameter, removeParameter, removeParameter, removeReaction, removeReaction, removeReaction, removeRule, removeRule, removeRule, removeSpecies, removeSpecies, removeSpecies, removeSpeciesType, removeSpeciesType, removeUnitDefinition, removeUnitDefinition, removeUnitDefinition, setAreaUnits, setAreaUnits, setAreaUnits, setConversionFactor, setConversionFactor, setExtentUnits, setExtentUnits, setExtentUnits, setLengthUnits, setLengthUnits, setLengthUnits, setListOfCompartments, setListOfCompartmentTypes, setListOfConstraints, setListOfEvents, setListOfFunctionDefinitions, setListOfInitialAssignments, setListOfParameters, setListOfReactions, setListOfRules, setListOfSpecies, setListOfSpeciesTypes, setListOfUnitDefinitions, setModelHistory, setSubstanceUnits, setSubstanceUnits, setSubstanceUnits, setTimeUnits, setTimeUnits, setTimeUnits, setVolumeUnits, setVolumeUnits, setVolumeUnits, unregister, unsetAreaUnits, unsetConversionFactor, unsetExtentUnits, unsetLengthUnits, unsetListOfCompartments, unsetListOfCompartmentTypes, unsetListOfConstraints, unsetListOfEvents, unsetListOfFunctionDefinitions, unsetListOfInitialAssignments, unsetListOfParameters, unsetListOfReactions, unsetListOfRules, unsetListOfSpecies, unsetListOfSpeciesTypes, unsetListOfUnitDefinitions, unsetModelHistory, unsetSubstanceUnits, unsetTimeUnits, unsetVolumeUnits, writeXMLAttributes
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm
addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet
public ModelDefinition()
ModelDefinition
instance.public ModelDefinition(int level, int version)
ModelDefinition
instance.level
- the SBML levelversion
- the SBML versionpublic ModelDefinition(Model model)
ModelDefinition
instance cloned from the given core Model
instance.model
- the core Model
to clonepublic ModelDefinition(java.lang.String id)
ModelDefinition
instance.id
- the idpublic ModelDefinition(java.lang.String id, int level, int version)
ModelDefinition
instance.id
- the idlevel
- the SBML levelversion
- the SBML versionpublic ModelDefinition clone()
SBase
SBase
with the same
properties
like this one.public void init()